I would appreciate some help with my data. I want to do Differential Expression profiling for miRNA samples.
Using the miRDeep2 program and algorithm, I'm in trouble when dealing with results to make a proper table in order to use it as input for DE software such as EdgeR or DEseq2.
Which .csv should be used for read count?
Also, there are duplicate values in the miRNA_expressed.csv. Should I consider the average or only one of them with highest value?
miRNA read_count precursor
ssc-let-7a 66271 ssc-let-7a-1
ssc-let-7a 66388 ssc-let-7a-2
ssc-let-7c 22747 ssc-let-7c